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September 9, 2009

Scientists Complete Genome Map Of Potato Famine Pathogen

by Sam Savage

A team of scientists has unraveled the entire genome of the pathogen that resulted in the Irish potato famine in the 1840s.

Scientists said the new genome map would help researchers in their fight against the same pathogen, which appears to be on the rise once again, as it still amounts for about $7 billion dollars in agricultural losses each year.

Writing in the journal Nature, the study was led by the Broad Institute of Harvard University and MIT, which worked alongside scientists from dozens of institutions.

"Scientists have studied this pathogen for 150 years and there's still a great deal we don't know about it," James Carrington, professor and director of the Center for Genome Research and Biocomputing at Oregon State University and collaborator on the project, said in a statement.

"It caused one of the most important famines in history and is still a major problem that costs billions of dollars to fight."

"This is probably the most costly plant pathogen, per acre, that we've ever had to deal with," said Nik Grunwald, a plant pathologist with the USDA's Agricultural Research Service.

"Part of the problem is that we've identified and can grow potatoes with resistance to late blight, but they aren't the varieties that the marketplace expects."

Co-lead author Sophien Kamoun, head of the Sainsbury Laboratory in Norwich, UK, said the map suggests a "two-speed" genome.

"Meaning that different parts of the genome are evolving at different rates," explained Kamoun.

"Future sequencing of additional strains and close relatives of this pathogen will help test this hypothesis and could transform our understanding of how it adapts to immune plants."

Scientists said that the pathogen is known for its ability to quickly change to new plant hosts even after some potatoes were bred to resist the P. infestans infection.

The new map allows researchers to uncover how the pathogen is able to adapt so quickly.

Scientists produced a high-quality genome sequence and compared it to the genomes of two relatives: P. sojae, which infects soybeans, and P. ramorum, which prefers oak and other trees and causes a condition known as sudden oak death.

They noted that P. infestans appears to be two and a half to four times the size of the other genomes by comparison.

Additionally, they noted that 75 percent of the genome's source of "added bulk" was made up of repetitive DNA.

"Such a large amount of repetitive DNA is pretty surprising, since there is a metabolic cost to maintain it," said senior author Chad Nusbaum, co-director of the Genome Sequencing and Analysis Program at the Broad Institute of MIT and Harvard.

"As a genome biologist, I have to wonder how the organism benefits from having it."

"We now have a comprehensive view of its genome, revealing the unusual properties that drive its remarkable adaptability," he added. "Hopefully, this knowledge can foster novel approaches to diagnose and respond to outbreaks."

Researchers said that additional studies would be necessary to determine how it will spread over time, but they are now equipped with the needed information thanks to the map's completion.